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The Specimen Data Refinery:A Canonical Workflow Framework and FAIR Digital Object Approach to Speeding up Digital Mobilisation of Natural History Collections

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Data Intelligence 2022年第2期4卷 320-341页

作者： Alex Hardisty paul Brack Carole Goble Laurence Livermore Ben scott Quentin Groom Stuart Owen Stian Soiland-Reyes School of Computer Science and Informatics Cardiff UniversityCardiff CF243AAUK The Department of Computer Science The University of ManchesterManchester M139PLUK The Natural History Museum London SW75BDUK Meise Botanic Garden 1860 MeiseBelgium Informatics Institute Faculty of ScienceUniversity of Amsterdam1090 GH AmsterdamThe Netherlands

A key limiting factor in organising and using information from physical specimens curated in natural science collections is making that information computable,with institutional digitization tending to focus more on imaging the specimens themselves than on efficiently capturing computable data about *** data are traditionally manually transcribed today with high cost and low throughput,rendering such a task constrained for many collection-holding institutions at current funding *** show how computer vision,optical character recognition,handwriting recognition,named entity recognition and language translation technologies can be implemented into canonical workflow component libraries with findable,accessible,interoperable,and reusable(FAIR)*** libraries are being developed in a cloudbased workflow plaform-the Specimen Data Refinery'(SDR)-founded on Galaxy workflow engine,Common Workflow Language,Research Object Crates(RO-Crate)and WorkflowHub *** SDR can be applied to specimens'labels and other artefacts,offering the prospect of greatly accelerated and more accurate data capture in computable *** kinds of FAIR Digital Objects(FDO)are created by packaging outputs of SDR workflows and workflow components as digital objects with metadata,a persistent identifier,and a specific type *** first kind of FDO are computable Digital Specimen(DS)objects that can be consumed/produced by workflows,and other applications.A single DS is the input data structure submitted to a workflow that is modified by each workflow component in turn to produce a refined DS at the *** Specimen Data Refinery provides a library of such components that can be used individually,or in *** cofunction,each library component describes the fields it requires from the DS and the fields it will in turn populate or *** second kind of FDO,RO-Crates gather and archive the diverse set of digital and real-world resources,configurations,a

关键词： Digital Specimen Workflow FAIR Digital Object RO-Crate

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Development of starch-based films reinforced with cellulosic nanocrystals and essential oil to extend the shelf life of red grapes

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Food Bioscience 2022年第3期47卷 403-412页

作者： Sneh Punia Bangar William scott Whiteside Fatih Ozogul Kyle D.Dunno George Armstrong Cavender paul Dawson Department of Food Nutrition and Packaging SciencesClemson UniversitySC 29634USA Department of Seafood Processing Technology Faculty of FisheriesCukurova UniversityBalcaliAdana01330Turkey Department of Packaging Science Rochester Institute of TechnologyRochesterNYUSA

Packaging material has an important role in extending the shelf-life of *** study investigated the effectiveness of cellulose nanocrystals(CNCs)derived from Kudzu(Pueraria montana)vine to reinforce to starch-based *** addition,the essential oil was incorporated into these nanocomposite films to evaluate further improvement in film properties and *** packaging materials,including the pearl millet starch(PMS),PMS reinforced with Kudzu CNCs,and PMS reinforced with Kudzu CNCs stabilized pickering emulsion containing clove bud oil(CBO),was used to develop biodegradable nanocomposite *** films were investigated for their thermal,morphological,mechanical,and barrier *** addition,the films were used as packaging material to improve the shelf life of the grapes for 15 days at 5℃.PMS films reinforced with Kudzu CNCs stabilized pickering emulsion of CBO were most effective in extending the shelf life of red grapes up to 15 days at 5℃ by maintaining the weight,firmness,and soluble solids in grapes for a longer duration during *** study suggests that PMS+Kudzu CNCs+EO films have the potential for commercial packaging of fruits during short storage periods without adversely affecting their quality and sensory attributes.

关键词： Packaging material Nanocomposites Cellulose nanocrystals Red grapes Shelf life

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The role of exosomes in peripheral nerve regeneration

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Neural Regeneration Research 2015年第5期10卷 743-747页

作者： Rosanna C.Ching paul j.Kingham Department of Integrative Medical Biology Umea University Department of Surgical & Perioperative Sciences Umea University

Peripheral nerve injuries remain problematic to treat, with poor functional recovery commonly observed. Injuries resulting in a nerve gap create specific difficulties for axonal regeneration. Approaches to address these difficulties include autologous nerve grafts （which are currently the gold standard treatment） and synthetic conduits, with the latter option being able to be im- pregnated with Schwann cells or stem cells which provide an appropriate micro-environment for neuronal regeneration to occur. Transplanting stem cells, however, infers additional risk of malignant transformation as well as manufacturing difficulties and ethical concerns, and the use of autologous nerve grafts and Schwann ceils requires the sacrifice of a functioning nerve. A new approach utilizing exosomes, secreted extracellular vesicles, could avoid these complications. In this review, we summarize the current literature on exosomes, and suggest how they could help to improve axonal regeneration following peripheral nerve injury.

关键词： axonal regeneration exosome extracellular vesicle microRNA microvesicle nerve gap neurite outgrowth peripheral nerve injury Schwann cell stem cell

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Species Concepts as Applied to the Whitefly Bemisia tabaci Systematics:How Many Species Are There?

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journal of Integrative Agriculture 2012年第2期11卷 176-186页

作者： LIU Shu-sheng john Colvin paul j De Barro Key Laboratory of Agricultural Entomology Ministry of Agriculture~Institute of lnsect Sciences Zhejiang University Hangzhou 310058 P.R. China Natural Resources Institute University of Greenwich Kent ME4 4TB United Kingdom CSIRO Ecosystem Sciences Brisbane QLD 4001 Australia

The worldwide distribution and extensive genetic diversity of the whitefly,Bemisia tabaci,has long been ***,the levels of separation within *** and the nomenclature of the various genetic groups have been a subject of *** phylogenetic analyses indicate that *** is a complex composed of 28 morphologically indistinguishable *** this article,we first review the debate and difficulties associated with ***＇s taxonomy and systematics,and argue for the need to apply the biological species concept in order to elucidate ***＇s *** summarize the accumulated genetic and behavioural data on reproductive incompatibilities evident amongst phylogenetic mtCOI groups of *** studies have been conducted with 14 of the 28 putative species covering 54 reciprocal inter-species pairs,and observations on mating behaviour have been conducted for seven species *** from both crossing trials and behavioural observations indicate a consistent pattern of reproductive isolation among the putative *** then discuss the technical and conceptual complexities associated with crossing experiments and behavioural observations designed to reveal reproductive ***,we elaborate on a strategy for further clarifying the pattern of reproductive isolation between *** groups and propose future research directions on the systematics of this complex.

关键词： whitefly systematics biological species cryptic species phylogenetic species reproductive isolation mating behavior taxonomy

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Selenoprotein expression is regulated at multiple levels in prostate cells

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Cell Research 2006年第12期16卷 940-948页

作者： Cheryl M Rebsch Frank j Penna Ⅲ paul R Copeland Department of Molecular Genetics Microbiology and immunology Department of Molecular Genetics Microbiology and immunologyThe Cancer Institute of New JerseyUMDNJ-Robert Wood Johnson Medical School675 Hoes LanePiscatawayNJ 08854USA

Selenium supplementation in a population with low basal blood selenium levels has been reported to decrease theincidence of several cancers including prostate *** on the clinical findings,it is likely that the antioxidantfunction of one or more selenoproteins is responsible for the chemopreventive effect,although low molecular weightseleno-compounds have also been posited to selectively induce apoptosis in transformed *** address the effects ofselenium supplementation on selenoprotein expression in prostate cells,we have undertaken an analysis of antioxidantselenoprotein expression as well as selenium toxicity in non-tumorigenic prostate epithelial cells(RWPE-1)and prostatecancer cells(LNCaP and PC-3).Our results show that two of the glutathione peroxidase family members(GPX1 andGPX4)are highly induced by supplemental selenium in prostate cancer cells but only slightly induced in RWPE-1 *** addition,GPX1 levels are dramatically lower in PC-3 cells as compared to RWPE-1 or LNCaP ***2 proteinand mRNA,however,are only detectable in RWPE-1 *** the three selenium compounds tested(sodium selenite,sodium selenate and selenomethionine),only sodium selenite shows toxicity in a physiological range of *** and in contrast to previous studies,RWPE-1 cells were significantly more sensitive to selenitethan either of the prostate cancer cell *** results demonstrate that selenoproteins and selenium metabolism areregulated at multiple levels in prostate cells.

关键词： prostate selenium selenoproteins glutathione peroxidase selenocysteine

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Limosilactobacillus mucosae FZjTZ26M3 prevents NAFLD in mice through modulation of lipid metabolism and gut microbiota dysbiosis

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Food Science and Human Wellness 2024年第3期13卷 1589-1601页

作者： Danting Dang Bowen Li Mengfan Ding Rpaul Ross Catherine Stanton jianxin Zhao Bo Yang Wei Chen State Key Laboratory of Food Science and Resources Jiangnan UniversityWuxi 214122China School of Food Science and Technology Jiangnan UniversityWuxi 214122China International joint Research Center for Probiotics&Gut Health Jiangnan UniversityWuxi 214122China APC Microbiome Ireland University College CorkCork T12 YT20Ireland Teagasc Food Research Centre MooreparkFermoyCork T12 YT20Ireland National Engineering Research Center for Functional Food Jiangnan UniversityWuxi 214122China

Lactobacillus are considered promising therapeutic methods for nonalcoholic fatty liver disease(NAFLD).The effects of two strains of Ltmosilactobacillus mucosae on NAFLD were investigated in this ***-old male C57BL/6j mice were divided into 4 groups(n=8 per group,Control,Model,FZjTZ26M3,FGSYC17L3).*** FZjTZ26M3 reduced the mice 's body weight,liver weight,and adipose tissue weight after 12 weeks of *** to serum analysis,total cholesterol,triacylglycerol,and low-density lipoprotein cholesterol significantly decreased after *** FZjTZ26M3 *** pathology showed that *** FZjTZ26M3 was effective to ameliorate lipid deposition in NAFLD ***,the expression of the gene related to lipid metabolism in the liver and adipose tissue was analyzed,and the results indicated that *** FZjTZ26M3 could alleviate NAFLD by regulating lipid ***,the results of 16S rRNA gene sequencing revealed a drop in the relative abundance of Ruminococcaceae,which is linked to inflammation,but the relative abundance of a potential probiotic Akkermansia significantly increased after *** FZjTZ26M3 ***,*** FZjTZ26M3 could be a candidate to prevent NAFLD.

关键词： Limosilactobacillus mucosae Nonalcoholic fatty liver disease(NAFLD) Probiotic Lipid metabolism Gut microbiota

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Globalization and Chinese Education in the Early 20th Century

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Frontiers of Education in China 2013年第3期8卷 398-419页

作者： paul j.BAILEY Department of History University of DurhamDurham DH13EXUK

With China’s growing significance in the global economy ever more evident,studies in recent years have highlighted multiple aspects of China’s“Globalization”(or global connections)that predate the contemporary *** article focuses on educational reform in the late Qing and early Republic as a way of illuminating a significant aspect of China’s Globalization during this *** particular,the article highlights the role of an emerging Chinese educational“lobby”that was involved in administration,teaching,and textbook compilation;furthermore,this lobby pioneered the introduction of new ideas,concepts,and innovative practice from abroad in the specialized journals on education-the first of their kind in China-which they edited and contributed *** significantly,contributors to these journals engaged with and discussed educational issues and problems that were simultaneously being debated in the *** the process Chinese educators and officials were able to draw upon,either to valorize or critique,a wide spectrum of contemporary foreign educational debate and practice in their prognosis of domestic education and its *** picture that emerges of Chinese education during this period is one in which Chinese educators perceived themselves very much as active participants in a global educational community.

关键词： Globalization nation-building educational reform Chinese educational lobby educational press

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A simulation program for demonstration and analysis of closed loop negative feedback control

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通讯和计算机（中英文版） 2009年第7期6卷 6-15页

作者： Thomas scott Deering paul Department of Industrial Technology Ohio University Athens 45701 USA

Increased emphasis on fuel consumption minimization and energy efficiency encourages more careful attention to control strategies for automobile vehicle systems. Simplified yet accurate simulation propulsion system models are needed to provide the control system designer an analytical platform for experimental assessment of novel and atypical control approaches. The structure of a simulation model for an automobile system including power train (energy supply) and propulsion (energy consumption) contributors is explained. This model has been developed for use in studying closed loop negative feedback control systems using ON/OFF, PID, and other control algorithms. Results from exercising the simulation model are illustrated for several vehicle operation scenarios, including steady state, acceleration, and deceleration, with future work targeted at terrain varying conditions. The approach to the development of the vehicle system model is explained, and examples of the dynamic operation of the model are provided. This model provides an easily modifiable process description that can be used to show visually and quantifiably the benefits and shortcomings of selected control strategies, as well as the influence of gain magnitudes on system stability and response. Further, this paper provides illustration of the model operation with a simple ON/OFF control strategy, as well as a straightforward proportional control strategy to demonstrate the potential of using the simulation model to produce useful results. Global energy efficiency parameters of merit are identified and sample calculations are provided to illustrate potential benefits of alternative strategies.

关键词：计算机仿真仿真程序模拟控制

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Cell Wall Microstructure Analysis Implicates Hemicellulose Polysaccharides in Cell Adhesion in Tomato Fruit Pericarp Parenchyma

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Molecular Plant 2009年第5期2卷 910-921页

作者： jose j. Ordaz-Ortiz Susan E. Marcus j. paul Knox Centre for Plant Sciences Faculty of Biological Sciences University of Leeds Leeds LS2 9JT United Kingdom

Methods developed to isolate intact cells from both unripe and ripe tomato fruit pericarp parenchyma have allowed the cell biological analysis of polysaccharide epitopes at the surface of separated cells. The LM7 pectic homogalacturonan epitope is a marker of the junctions of adhesion planes and intercellular spaces in parenchyma systems. The LM7 epitope persistently marked the former edge of adhesion planes at the surface of cells separated from unripe and ripened tomato fruit and also from fruits with the Cnr mutation. The LM 11 xylan epitope was associated, in sections, with cell walls lining intercellular space but the epitope was not detected at the surface of isolated cells, being lost during cell isolation. The LM15 xyloglucan epitope was present at the surface of cells isolated from unripe fruit in a pattern reflecting the former edge of cell adhesion planes/intercellular space but with gaps and apparent breaks. An equivalent pattern of LM15 epitope occurrence was revealed at the surface of cells isolated by pectate lyase action but was not present in cells isolated from ripe fruit or from Cnr fruit. In contrast to wild-type cells, the LM5 galactan and LM21 mannan epitopes occurred predominantly in positions reflecting intercellular space in Cnr, suggesting a concerted alteration in cell wall microstructure in response to this mutation. Galactanase and mannanase, along with pectic homogalacturonan-degrading enzymes, were capable of releasing cells from unripe fruit parenchyma. These observations indicate that hemicellulose polymers are present in architectural contexts reflecting cell adhesion and that several cell wall polysaccharide classes are likely to contribute to cell adhesion/cell separation in tomato fruit pericarp parenchyma.

关键词： Cell walls fruit development tomato cell adhesion cell separation polysaccharide.

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Cell Wall Biology： Perspectives from Cell Wall Imaging

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Molecular Plant 2011年第2期4卷 212-219页

作者： Kieran j.D. Lee Susan E. Marcus j. paul Knox Centre for Plant Sciences Faculty of Biological Sciences University of Leeds Leeds LS2 9JT UK

Polysaccharide-rich plant cell walls are important biomaterials that underpin plant growth, are major repositories for photosynthetically accumulated carbon, and, in addition, impact greatly on the human use of plants. Land plant cell walls contain in the region of a dozen major polysaccharide structures that are mostly encompassed by cellulose, hemicelluloses, and pectic polysaccharides. During the evolution of land plants, polysaccharide diversification appears to have largely involved structural elaboration and diversification within these polysaccharide groups. Cell wall chemistry is well advanced and a current phase of cell wall science is aimed at placing the complex polysaccharide chemistry in cellular contexts and developing a detailed understanding of cell wall biology. Imaging cell wall glycomes is a challenging area but recent developments in the establishment of cell wall molecular probe panels and their use in high throughput procedures are leading to rapid advances in the molecular understanding of the spatial heterogeneity of individual cell walls and also cell wall differences at taxonomic levels. The challenge now is to integrate this knowledge of cell wall heterogeneity with an understanding of the molecular and physiological mechanisms that underpin cell wall properties and functions.

关键词： Cell structure cell walls fluorescence imaging development cell wall imaging polysaccharides

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